9/22/2009 @ 6:00PM

Cheap DNA Sequencing

In 2003, a Harvard Ph.D. committee denied Jay Shendure permission to graduate. There was no coherent theme to his research, he was told. “I almost got angry,” says the 34-year-old Shendure, now an assistant professor at the University of Washington. “[Instead] I channeled all of my energy into one particular thing and it ended up being a watershed year.”

It was that year that he made the first steps toward a new approach that could make DNA sequencing cheaper and faster by allowing researchers to focus on the 1% of the 3-billion-letter human genome that they care most about.

It comes at an ideal time since there’s a race to drive down the cost of sequencing genes. Between 1990 and 2003, the Department of Energy’s Human Genome Project spent $2.7 billion to sequence what amounted to half the code for a person. Now the biotech company
Illumina
will sequence your genome for less than $50,000. But researchers hope to one day spend as little as $1,000 per person, thereby allowing them to conduct studies comparing the genomes of thousands of people at once.

Shendure’s solution: just sequence the 20,000 genes that code for proteins, which are the basic building blocks for life. Shendure slices up the genome and runs it over a microscope slide where known portions of the protein genes are attached. The relevant code sticks like Velcro. The process is repeated until nearly all the gene fragments on the slide have stuff stuck to them. Then, he sequences that.

He co-authored a proof-of-concept paper in Nature in August and wants to apply the technology to thousands of genomes in the next round of research. If successful, Shendure says it will cost about $2,500 per person.

One person who is excited is George Church, the Harvard Medical School professor famous for his pioneering genetic work–and Shendure’s former thesis adviser. “He was willing to question almost every aspect of what we did,” says Church. “He took a risk and defined that field and now he’s done it again.”